microcat init

!microcat init -h

Usage: microcat init [OPTIONS] COMMAND [ARGS]...

  Init microcat style analysis project

Options:
  -h, --help  Show this message and exit.

Commands:
  bulk     Bulk seq microbiome mining pipeline init.
  multi    Single-cell RNA-seq microbiome mining pipeline init.
  sims     Simulation
  single   Single-cell RNA-seq microbiome mining pipeline init.
  spatial  Single-cell RNA-seq microbiome mining pipeline init.

microcat init single

!microcat init single -h

Usage: microcat init single [OPTIONS]

  Single-cell RNA-seq microbiome mining pipeline init.

  Init 10x Genomics Example:

  $ microcat init single --host starsolo --chemistry tenx_auto --classifier
  kraken2uniq

  Init Smartseq2 Example:

  $ microcat init single --host starsolo --chemistry smartseq2 --classifier
  kraken2uniq

Options:
  -b, --begin [host|classifier|denosing]
                                  Pipeline starting point  [default: host]
  --host [starsolo|cellranger]    Which hoster used  [default: starsolo]
  --chemistry [smartseq|smartseq2|tenx_3pv1|tenx_3pv2|tenx_3pv3|seqwell|tenx_auto|dropseq|tenx_multiome|tenx_5ppe|seqwell|indrop_v1|indrop_v2|celseq2|cb_umi_simple|cb_umi_complex]
                                  Sequencing chemistry option, required when
                                  host is starsolo  [default: tenx_auto]
  --classifier [kraken2uniq|krakenuniq|pathseq|metaphlan]
                                  Which classifier used  [default:
                                  kraken2uniq]
  --align [bowtie2|bwa|minimap2|bwa2|mm2plus]
                                  Which align used
  --cellbender                    Use CellBender for single-cell environment
                                  RNA filtering
  --gpu                           Use GPU for CellBender acceleration (enabled
                                  only if --cellbender is true)
  -s, --samples PATH              Samples list, tsv format required.
  -d, --workdir WORKDIR           Project workdir
  -p, --project_name PROJECT_NAME
                                  Project name
  -h, --help                      Show this message and exit.

microcat init spatial

!microcat init spatial -h

Usage: microcat init spatial [OPTIONS]

  Single-cell RNA-seq microbiome mining pipeline init.

Options:
  --begin [simulate|trimming|host|classifier|denosing]
                                  Pipeline starting point  [default: trimming]
  --host [starsolo|cellranger]    Which hoster used  [default: starsolo]
  --chemistry [smartseq|smartseq2|tenx_3pv1|tenx_3pv2|tenx_3pv3|seqwell|tenx_auto|dropseq|tenx_multiome|tenx_5ppe|seqwell|celseq2]
                                  Sequencing chemistry option, required when
                                  host is starsolo
  --classifier [kraken2uniq|krakenuniq|pathseq|metaphlan]
                                  Which classifier used  [default: pathseq]
  -s, --samples PATH              Samples list, tsv format required.
  -h, --help                      Show this message and exit.